However, even if the project is split into two distinct partitions of ECMA-based and non-ECMA components, how easy is it going to be for the third part developers adding components to the ECMA-based partition to know that he is not treading on Microsoft's patents by implementing functionality defined in Microsoft's .NET patents?

Although there is prior art examples of individual technologies such as the JVM etc, Microsoft patents such as the one mentioned, define and claim the interoperation of the components and the .NET platform.

There is NO way to work-around the issue, no amount of renaming the API calls or reimplementing the methords used will invalidate the patents.